Experiment: 3NP0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DAT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.959	α = 90
b = 180.959	β = 90
c = 180.959	γ = 90

Symmetry
Space Group	F 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2009-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.48	30	98.3	0.064		9.8		41911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.48	1.53	88.7		0.286		4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1DAT	1.48	19.29	39184	2070	96.82	0.19895	0.19841	0.20954	RANDOM	16.578

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.985
r_dihedral_angle_4_deg	17.91
r_dihedral_angle_3_deg	14.19
r_dihedral_angle_1_deg	4.479
r_scangle_it	3.069
r_scbond_it	1.82
r_angle_refined_deg	1.613
r_mcangle_it	1.172
r_mcbond_it	0.65
r_chiral_restr	0.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.985
r_dihedral_angle_4_deg	17.91
r_dihedral_angle_3_deg	14.19
r_dihedral_angle_1_deg	4.479
r_scangle_it	3.069
r_scbond_it	1.82
r_angle_refined_deg	1.613
r_mcangle_it	1.172
r_mcbond_it	0.65
r_chiral_restr	0.357
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1364
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	67

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.